Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions. (Q35608554)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25223953%20AND%20SRC:MED&resulttype=core&format=json

16 February 2020

title

Mechanistic insights into RNA transphosphorylation from kinetic isotope effects and linear free energy relationships of model reactions (English)

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16 February 2020

4

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Darrin M York

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1

Haoyuan Chen

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16 February 2020

author name string

Timothy J Giese

series ordinal

2

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16 February 2020

Ming Huang

series ordinal

3

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16 February 2020

Michael E Harris

series ordinal

5

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16 February 2020

language of work or name

English

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publication date

15 September 2014

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Chemistry—A European Journal

16 February 2020

published in

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16 February 2020

volume

20

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issue

44

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16 February 2020

page(s)

14336-14343

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Theoretical Modeling on the Reaction Mechanism of p-Nitrophenylmethylphosphate Alkaline Hydrolysis and its Kinetic Isotope Effects

16 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Linear free energy relationships in RNA transesterification: theoretical models to aid experimental interpretations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2'-O-transphosphorylation

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Why nature really chose phosphate

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP supe

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Characterization of the reaction path and transition states for RNA transphosphorylation models from theory and experiment

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Biological phosphoryl-transfer reactions: understanding mechanism and catalysis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Catalytic strategies of self-cleaving ribozymes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Enzymatic mechanisms of phosphate and sulfate transfer.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Satellite tobacco ringspot virus RNA: A subset of the RNA sequence is sufficient for autolytic processing

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Control of gene expression by a natural metabolite-responsive ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Isotope effects in the study of phosphoryl and sulfuryl transfer reactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Enzyme-Catalyzed Phosphoryl Transfer Reactions

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Antigenomic RNA of human hepatitis delta virus can undergo self-cleavage.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Why nature chose phosphates

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

A site-specific self-cleavage reaction performed by a novel RNA in Neurospora mitochondria

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Hammerhead ribozymes: true metal or nucleobase catalysis? Where is the catalytic power from?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Kinetic Isotope Effects for RNA Cleavage by 2′-O- Transphosphorylation: Nucleophilic Activation by Specific Base

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Continuous surface charge polarizable continuum models of solvation. I. General formalism.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Parameters for the Description of Transition States

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Supermolecule density functional calculations suggest a key role for solvent in alkaline hydrolysis of p-nitrophenyl phosphate.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Thermodynamic origin of the increased rate of hydrolysis of phosphate and phosphorothioate esters in DMSO/water mixtures

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Quantum mechanical continuum solvation models.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

A concerted mechanism for the transfer of the thiophosphinoyl group from aryl dimethylphosphinothioate esters to oxyanionic nucleophiles in aqueous solution

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Compelling evidence for a stepwise mechanism of the alkaline cyclisation of uridine 3'-phosphate esters

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Comparisons of phosphorothioate with phosphate transfer reactions for a monoester, diester, and triester: isotope effect studies

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Evidence for direct attack by hydroxide in phosphodiester hydrolysis

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4432475

Density-functional thermochemistry. III. The role of exact exchange

25 September 2018

1 reference

https://api.crossref.org/works/10.1002%2FCHEM.201403862

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCHEM.201403862

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCHEM.201403862

Atomic Radii and Interatomic Distances in Metals

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCHEM.201403862

Cα−H Bond-Stretching Frequency in Alcohols as a Probe of Hydrogen-Bonding Strength: A Combined Vibrational Spectroscopic and Theoretical Study ofn-[1-D]Propanol

21 January 2018

1 reference

https://api.crossref.org/works/10.1002%2FCHEM.201403862

1JCH correlates with alcohol hydrogen bond strength

21 January 2018

1 reference

12 December 2020

Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases

1 reference

12 December 2020

Transesterification thio effects of phosphate diesters: free energy barriers and kinetic and equilibrium isotope effects from density-functional theory

1 reference

12 December 2020

Cα–H Carries Information of a Hydrogen Bond Involving the Geminal Hydroxyl Group: A Case Study with a Hydrogen-Bonded Complex of 1,1,1,3,3,3-Hexafluoro-2-propanol and Tertiary Amines

1 reference

12 December 2020

Identifiers

DOI

10.1002/CHEM.201403862

1 reference

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16 February 2020

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16 February 2020

PubMed publication ID

25223953

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